When the evil Shadow Line begins to use their evil train the Kleiner to kidnap children, a young man named Right is amongst those nearly captured. He then sees the prismatic Rainbow Line and its Ressha trains appear, along with four of the ToQgers, inspiring him to help protect the children with them.

The ToQgers arrive at a train station taken over by the Shadow Line which has been renamed "Kettougahara", controlled by the Shadow Line's Saber Shadow who makes everyone duel. The ToQgers do their hardest to protect a boy who is scared at what the Shadow Line has done to his neighborhood and figure out a way to end the Shadow Line's control.

After Ticket warns the ToQgers that the Ressha trains will not wait for them, Kagura is left behind and despite her fears must take on Chain Shadow by herself.

When having some time off at a station stop, Tokatti loses his Rainbow Pass somewhere, forcing him to follow the others on standard forms of transportation. While Right, Hikari, and Kagura battle Stove Shadow, Mio helps Tokatti search for his missing pass.

The Rainbow Line makes an abrupt stop at a river, requiring the use of the Car Carrier Ressha to cross, but their Imagination is not enough to power it. As the other ToQgers try to come up with a way to cross, Bucket Shadow starts to collect darkness by making people feel hungry via eating every scrap of food from them.

Right managed to find one of the missing Support Ressha while out in the woods, so he and Tokatti go out to find it. However, General Schwarz has been spying on the ToQgers and heads out to capture the Support Ressha for the Shadow Line.

After getting too emotionally involved in a ninja movie, Kagura accidentally breaks Hikari's kendama toy, and thinks that he won't forgive her. However, the Ressha stops at a new Dark Station where Hanko Shadow has made everyone lose their motivation, and Right, Tokatti, and Mio fall under his spell.

The signal from the lost Diesel Ressha is found, but because it is so weak there might be a chance it cannot work again. Right is sent out to find it, as his strong Imagination can restore it. They learned that the previous enemy they encountered placed a bomb on Tokatti that is strong enough to destroy the Resshas, when the Ressha's brakes are discovered to be broken, everyone fears that the Shadow Line has planted a bomb on them.

While the Ressha are under maintenance from the previous battle, the group uses the Support Ressha. At the next stop, Right wants to try a new buffet, but Mio meets someone apparently from her past who was in love with her.

After Tokatti meets a young man named Hiroki Fujisawa who seems to be unable to see the Ressha, Type Shadow sentences Tokatti to die at sunset.

While the ToQgers enjoy a day out at an amusement park, Right meets a young man with balloons who seems odd. Baron Nero leads an offensive against them in order to welcome the Emperor of Darkness onto the Shadow Line, and also has a particular interest in the man with the balloons.

The other ToQgers can no longer see the Ressha and are seemingly devoid of their Imagination. Right tries to get through to them, but Lamp Shadow reveals to him that Z has hypnotized all of them to forget their time on the Rainbow Line. Right must figure out how to get them back to normal, while also dealing with new memories of their childhood home.

The Conductor reveals that he has commissioned the transformation items for the sixth ToQger, and a Rainbow Line maintenance worker named Zaram, a former member of the Shadow Line, has not been chosen to be ToQ 6gou.

Although Zaram has left the Shadow Line and has become ToQ 6gou, he does not wish to remain with the ToQgers. When Ring Shadow traps people by putting rings with their names on their heads, Zaram, who should have eschewed his old Shadow name, must find a way to help the ToQgers and escape his former shackles as a Shadow.

While Tokatti is trying to befriend Akira, the Ressha gets trapped in a mine collapse orchestrated by a Kurainer Robo, forcing Tokatti and Akira to work together to find ToQ 6gou's personal Ressha.

Jack-in-the-Box Shadow's ability to send people flying away from him if they laugh affects all the ToQgers except Akira, leading the others to help Akira find his sense of humor or else he may be killed.

Soap Shadow's ability to switch people's minds and bodies switches Gritta and Mio just as Gritta is to be married to Emperor Z.

Mio suddenly recovers a memory of their hometown, in that around this time of year they had a festival for the stars, and Right remembers as well. As they search for their hometown, the wedding of Emperor Z and Miss Gritta commences, and General Schwarz takes over the Ressha in the ToQgers' absence.

The ToQgers must defeat Miss Gritta and General Schwarz while trying to recover their memories of their long lost home town.

To find their hometown Subarugahama, the ToQgers must move the Ressha onto the Shadow Line to free it from the darkness engulfing it, but the shadows engulfing the junction point keeps them from using their powers

In the next Shadow Town, the ToQgers come across various fictional characters, with Tokatti's favorite childhood superhero Ryo Knight appearing before him to encourage him, but all is not as it seems.

Right tries to use the Hyper Ressha to liberate the next Shadow Town, but his body cannot handle the strain. Elsewhere, new members of the Shadow Line appear.

Madame Noir uses her powers to turn Right against the other ToQgers, with Tokatti leading the group to get their friend back.

The ToQgers travel to the Hyper Ressha Terminal to meet the Rainbow Line President, and Emperor of Darkness Z decides to take the opportunity to take over the terminal himself.

After the President of the Rainbow Line disbands the ToQgers, Right feels he is wrong and insists that he and the others continue the fight against the Shadow Line.

With their memories back, Right and Hikari must use their training in karate from Right's grandfather to defeat a Shadow Monster who has turned the people around the next Dark Station into his fighters, rather than Kuros.

With the Hyper Ressha Terminal occupied by the Shadow Line forces, the President decides to authorize the ToQgers to use all thirteen of their Ressha together to get it back, but first, they must get the Drill Ressha back from General Schwarz.

With Christmas approaching, Imagination begins to run wild which makes the Shadow Line weaker. Right, however, realizes Akira is missing, while General Schwarz plans an offensive against Emperor Z and various defeated Shadow Creeps suddenly revive one after another.

Akira, as Zaram, joins General Schwarz in his assault on Castle Terminal, but someone else gets the AppliChanger and attacks the ToQgers as ToQ 6gou.

Subarugahama is discovered to be kept under the Castle Terminal, leading the ToQgers to attempt an assault on the castle in order to free their hometown.

Right wants to make an assault on Castle Terminal to free Subarugahama, but Akira and Mio realize that he is being too headstrong. Wagon reveals that she can deliver a letter for them, but it must contain their true feelings of things and Tokatti is not ready to commit to that.

When Dollhouse Shadow attacks the ToQgers, Hikari and Kagura are trapped inside its dollhouse which will burn and kill them if they cannot find a way out or if the others cannot stop it.

Miss Gritta helps the ToQgers reach Castle Terminal to save their hometown, but Emperor Z still stands in their way.

The ToQgers have managed to free Subarugahama and Tokatti has figured out a way for them to become children again, but Right is not sure what to do after transforming into Dark ToQ 1gou in his fight with Emperor Z.

Akira stops Right from taking on Emperor Z as Dark ToQ 1gou on his own as he fears for his safety and promises to fight by Right's side. Elsewhere, the other ToQgers, as children once more, go to their secret base and find something completely unexpected.

The massive monster’s darkness has engulfed Right, the other ToQgers on the Resshas and the whole city. Right cannot face Zed even using the darkness and he is unable to imagine himself being victorious. Just when he has run out of options, the other ToQgers appear to save him. Then, among the darkness they can see the lights of the lamps for the Star Festival.